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Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms.

Bertolini F, Scimone C, Geraci C, Schiavo G, Utzeri VJ, Chiofalo V, Fontanesi L - PLoS ONE (2015)

Bottom Line: Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca).Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads.The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources.

View Article: PubMed Central - PubMed

Affiliation: Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy; Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, Messina, Italy.

ABSTRACT
Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources.

No MeSH data available.


Nucleotide divergence between horse and donkey genomes: distribution of divergence rates in 1-Mb chromosome regions designed on the EcuCab2.0 genome version.Autosomal windows are in blue and chromosome X windows are in red.
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pone.0131925.g003: Nucleotide divergence between horse and donkey genomes: distribution of divergence rates in 1-Mb chromosome regions designed on the EcuCab2.0 genome version.Autosomal windows are in blue and chromosome X windows are in red.

Mentions: Considering only fixed single nucleotide differences between the EquCab2.0 genome and the obtained Ion Proton donkey sequences, a total of about 18.28 million positions were different between the two species. If we use only Illumina reads obtained from Willy [36], the number of differences with the EquCab2.0 genome was about 22.12 M, similar to what obtained with the Ion Proton. We were a little bit more stringent than Orlando et al. [36] who reported about 23.8 M of different positions. S3 Table also reports the detailed information separated for the different horse chromosomes. S1 Fig shows the averaged density of differences between the horse and donkey genomes across chromosomes whereas Figs 3 and 4 show the distribution of divergence rates in 1-Mb chromosome regions designed on the EcuCab2.0 genome version. If we combine the three sequenced donkey genomes (two that we sequenced with Ion Proton and one obtained with Illumina [36]), the number of fixed positions were reduced to a total of about 15.9 million, that means that genome wide nucleotide divergence α between E. caballus and E. asinus could be ~0.67%. However, it could be possible that a fraction of the fixed differences might be polymorphic in donkey as well as in horse, reducing this estimation of about 0.10–0.15%, depending on the effective population size of the two species (reaching a level of ~ 0.52–0.57% of nucleotide divergence between these species; see also below the identification of SNPs). This number is lower than that reported between the human and chimpanzee genomes and obtained from a more extensive analysis (1.06%) [54], two species that diverged about 6–7 Myr BP [54, 55]. The genome wide nucleotide divergence between horse and donkey, as roughly estimated in our study, reflects the more recent differentiation of these two species (4.0–4.5 Myr BP [36]) than what estimated as time of divergence between the human and the chimpanzee lineages. Orlando et al. [36] also suggested slower mutation rates in horse than human. Based on this, and comparing the human-chimpanzee nucleotide divergence, our estimation of about 0.52%-0.57% of differences between horse and donkey seems to fit well the Equus most recent common ancestor living about 4.0–4.5 Myr BP [36].


Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms.

Bertolini F, Scimone C, Geraci C, Schiavo G, Utzeri VJ, Chiofalo V, Fontanesi L - PLoS ONE (2015)

Nucleotide divergence between horse and donkey genomes: distribution of divergence rates in 1-Mb chromosome regions designed on the EcuCab2.0 genome version.Autosomal windows are in blue and chromosome X windows are in red.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4495037&req=5

pone.0131925.g003: Nucleotide divergence between horse and donkey genomes: distribution of divergence rates in 1-Mb chromosome regions designed on the EcuCab2.0 genome version.Autosomal windows are in blue and chromosome X windows are in red.
Mentions: Considering only fixed single nucleotide differences between the EquCab2.0 genome and the obtained Ion Proton donkey sequences, a total of about 18.28 million positions were different between the two species. If we use only Illumina reads obtained from Willy [36], the number of differences with the EquCab2.0 genome was about 22.12 M, similar to what obtained with the Ion Proton. We were a little bit more stringent than Orlando et al. [36] who reported about 23.8 M of different positions. S3 Table also reports the detailed information separated for the different horse chromosomes. S1 Fig shows the averaged density of differences between the horse and donkey genomes across chromosomes whereas Figs 3 and 4 show the distribution of divergence rates in 1-Mb chromosome regions designed on the EcuCab2.0 genome version. If we combine the three sequenced donkey genomes (two that we sequenced with Ion Proton and one obtained with Illumina [36]), the number of fixed positions were reduced to a total of about 15.9 million, that means that genome wide nucleotide divergence α between E. caballus and E. asinus could be ~0.67%. However, it could be possible that a fraction of the fixed differences might be polymorphic in donkey as well as in horse, reducing this estimation of about 0.10–0.15%, depending on the effective population size of the two species (reaching a level of ~ 0.52–0.57% of nucleotide divergence between these species; see also below the identification of SNPs). This number is lower than that reported between the human and chimpanzee genomes and obtained from a more extensive analysis (1.06%) [54], two species that diverged about 6–7 Myr BP [54, 55]. The genome wide nucleotide divergence between horse and donkey, as roughly estimated in our study, reflects the more recent differentiation of these two species (4.0–4.5 Myr BP [36]) than what estimated as time of divergence between the human and the chimpanzee lineages. Orlando et al. [36] also suggested slower mutation rates in horse than human. Based on this, and comparing the human-chimpanzee nucleotide divergence, our estimation of about 0.52%-0.57% of differences between horse and donkey seems to fit well the Equus most recent common ancestor living about 4.0–4.5 Myr BP [36].

Bottom Line: Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca).Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads.The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources.

View Article: PubMed Central - PubMed

Affiliation: Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy; Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, Messina, Italy.

ABSTRACT
Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources.

No MeSH data available.